The vertebrate genome contains a predicted 100,000 genes, most of unknown function. The recent development of morpholino-based gene knockdown technology in zebrafish has opened the door to the genome-wide assignment of function based on sequence in a model vertebrate. We propose to explore the molecular mechanisms that control fundamental vertebrate embryonic processes of patterning and organ formation, biological problems in which cell-cell communication is critical during development. We will focus this study on the systematic assignment of biological function to a set of 100-200 putative secreted proteins to identify key players in these intercellular embryonic signaling cascades. We will accomplish this goal through the following specific aims: Aim I. Development of a secreted protein morpholino core database. Genes encoding predicted secreted proteins will be selected through analysis of the zebrafish genomic and EST database. Morpholinos targeted to these genes will be generated and examined for function in the following biological processes: Aim II. Isolation of secreted proteins required for early embryonic and neural patterning. Aim III. Isolation of secreted proteins required for cardiovascular and sensory organ formation. Aim IV. Isolation of secreted proteins required for digestive organ formation and function. The identification of molecules required for vertebrate patterning and organ formation has critical implications for the understanding of genetic deficiencies in these processes. In addition, these signaling proteins, crucial for development in vivo, will be crucial to the establishment of conditions for in vitro organ formation. The zebrafish offers the first comprehensive analysis of these processes using as template an entire vertebrate genome.